Recycling the cartons. Even Milk doesn't do that.
"Milk cartons are heavily waxed. This makes them difficult if not impossible to recycle." Correction: Milk cartons are a layer of low density polyethylene on both faces of cardboard.
Overcoming the costs of two way transport for the carton containers.
Milk is shipped in cartons which in turn are in plastic crates. The crates make the round trip. Milk is usually not tranported long distances.
Water bottles are on cardboard flats, shrink wrapped with more plastic. Most of them end up in the land fill. A water truck goes the other way with a new cargo.
Overcoming the bad press of replacing a bad packaging system with one even less sustainable.
This article http://www.slate.com/articles/health_and_science/the_green_lantern/2011/03/disoriented_in_the_dairy_aisle.html
points out that a plastic milk jug is 4 oz, a cardboard carton is 5 oz. The plastic is an easier recycle.
Glass is your best option. Apparently even with the high energy cost of fusing silica and lime into glass, it's still about half the energy cost of either plastic or cardboard. But it may be as much as 1/3 of the shipping weight. Slate's article claimed that over the life of a milk bottle the energy cost was about 1/2 of the other two.
Now Slate's article was about milk -- much better re-use rate generally.
At one point you could get 'bag' milk. 1 liter in a polyethylene bag. This was the most sustainable one-way packaging possible. A small amount of PE. PE is one of the most recycleable plastics. The current use of PE milk jugs is close behind, and is certainly better than cardboard cartons.
There is a case to be made for glass bottles. With milk especially, as the crates go back anyway, and washing bottles on a large scale works quite well.
Putting water in containers is where the non-sustainability starts. Why should water cost more than gasoline?